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When I remove the bad lines from the startup in msconfig, will that also remove the corresponding lines in the registry?

It puts the lines in a different place, so if you check one you shouldn't have, you can undo it. Usually. There's one I came across that replaced a security file of some sort, and I couldn't restart the computer without one or the other. That was one of those 1/4 . I"m more careful googling them now... The registry location varies (naturally) depending on the version of windows.

-jk